What is the Difference Between ITS1 and ITS2

The key difference between ITS1 and ITS2 is that ITS1 is a spacer DNA located between 18S and 5.8S rRNA genes in eukaryotes, while ITS2 is a spacer DNA located between 5.8S and 28S rRNA genes in eukaryotes.

Internal transcribed spacer (ITS) is the spacer DNA usually located between small subunit ribosomal RNA and large subunit ribosomal RNA genes in the chromosome or in the corresponding transcribed region in the polycistronic rRNA precursor transcript molecule. In bacteria and archaea, there is only a single ITS between 16S and 23S rRNA genes. But in eukaryotes, there are two ITS spacer DNA: ITS1 (between 18S and 5.8S rRNA genes) and ITS2 (between 5.8S and 28S rRNA). Therefore, ITS1 and ITS2 are two spacer DNA found between rRNA genes in eukaryotes.

CONTENTS

1. Overview and Key Difference
2. What is ITS1 
3. What is ITS2
4. Similarities – ITS1 and ITS2
5. ITS1 vs ITS2 in Tabular Form
6. Summary

What is ITS1?

ITS1 is a spacer DNA located between 18S and 5.8S rRNA genes in eukaryotes. ITS refers to a piece of nonfunctional spacer DNA located between rRNA genes. ITS1 has a greater length variation than ITS2. The length variation of ITS1 is approximately (200-300bp). ITS markers such as ITS1 have proven their efficiency in elucidating phylogenetic relationships among different taxa. Moreover, ITS1 spacer DNA is less conserved than ITS2 spacer DNA. ITS1 structures are only conserved in much smaller taxonomic units. Each eukaryotic ribosomal cluster also contains regions called external transcribed spacers (5’ and 3’ ETS).

The ITS1 spacer DNA is very close to the 5’external transcribed spacer (5’ ETS). Furthermore, if anyone wants to amplify the ITS1 region for phylogenetic relationship studies, they have to use a specific primer pair (reverse and forward primers) for this purpose. To amplify ITS1 region, two primer sets are normally used in the PCR protocols of laboratories. They are ITS1 forward and ITS2 reverse or ITS1 foward and ITS4 reverse.

What is ITS2?

ITS2 is a spacer DNA located between 5.8S and 28S rRNA genes in eukaryotes. ITS2 region has a shorter length variation than the ITS1 region. The length variation of ITS2 is approximately (180-240bp). However, ITS2 region is more conserved than ITS1 region in many taxonomic units. It identifies that all ITS2 sequences share a common core of the secondary structure. Moreover, 40% ITS2 region is conserved among all angiosperms, while it is possible to align 50% of the ITS2 region across family and higher level.

Regardless of the scope of conservation, usage of ITS2 region also very popular such as ITS1 region in phylogenetic relationship studies, especially in fungal DNA barcoding. To amplify ITS2 region, a specific primer set is generally used in the PCR protocols of laboratories. That is ITS1 foward and ITS4 reverse. But when PCR protocol uses this primer set, it also amplifies ITS1 region together with the ITS2 region. Further, the ITS2 spacer DNA is very close to the 3’external transcribed spacer (3’ ETS).

Similarities Between ITS1 and ITS2

• ITS1 and ITS2 are two spacer DNA located between rRNA genes.
• They are present only in eukaryotes.
• Both can be amplified by using specific primer pairs.
• They are both excised in rRNA maturation as non-functional by-products.
• Both are very important for phylogenetic relationship studies, especially in fungal DNA barcoding.

Difference Between ITS1 and ITS2

ITS1 is a spacer DNA present between 18S and 5.8S rRNA genes in eukaryotes while ITS2 is a spacer DNA located between 5.8S and 28S rRNA genes in eukaryotes. So, this is the key difference between ITS1 and ITS2. Furthermore, ITS1 has greater length variation compared to ITS2. On the other hand, ITS2 has a shorter length variation compared to ITS1. This is another difference between ITS1 and ITS2.

The below infographic lists the differences between ITS1 and ITS2 in tabular form for side by side comparison.

Summary – ITS1 vs ITS2

Internal transcribed region (ITS) is a non-functional piece of spacer DNA located between rRNA genes. In bacteria and archaea, there is only a single ITS region. But in eukaryotes, there are two ITS regions: ITS1 and ITS2. ITS1 is a spacer DNA that is located between 18S and 5.8S rRNA genes in eukaryotes, while ITS2 is a spacer DNA that is located between 5.8S and 28S rRNA genes in eukaryotes. Thus, this is the summary of the difference between ITS1 and ITS2.

Reference:

1. “Internal Transcribed Spacer.” An Overview | ScienceDirect Topics.
2. Schoch, Conrad L., et al. “Nuclear Ribosomal Internal Transcribed Spacer (ITS) Region as a Universal DNA Barcode Marker for Fungi.” PNAS, National Academy of Sciences.

Image Courtesy:

1. “Eucaryot rdna” By – Pharaoh han assumed – No machine-readable source provided. Own work assumed (based on copyright claims) (CC BY-SA 3.0) via Commons Wikimedia
2. “MolecularMarkersSymbiodinium” By Allisonmlewis – Own work (CC BY-SA 4.0) via Commons Wikimedia